Search for fermentation metabolites in MSV000084900

Introduction

The fermented foods residency group at the Astera Institute wanted to search for a set of metabolites in an existing public dataset: MassIVE MSV000084900 GNPS Global Foodomics dataset 3500 (“Metabolite analysis of 3,500 food and beverage samples, ethanol extraction. Data were acquired using a Bruker Daltonics maXis Impact and C18 RP-UHPLC. Positive polarity acquisition of LC-MS/MS.”). Prior to this analysis we evaluated that list for likelihood of detection in the dataset, and found that almost all of the metabolites of interest were low molecular weight and polar which would lend to less retention on C18 columns (potential to elute before MS scans begin), and many were much more likely to be detected in negative ion mode than positive mode (dataset collected in positive mode only). It was decided to proceed to search for the metabolite of interest and this notebook is the result of that search for these analytes across the 3,500 mzXMLs using the GNPS2 platform.

Click to show table of Metabolites of Interest

Metabolite of Interest	InChI Key	PubChem CID	Formula	Monoisotopic Mass	Chemical Structure	GNPS Library Entries (Positive)	GNPS Library Entries (Negative)	All Adducts (Positive)	All Ion Sources (Positive)	All Instruments (Positive)	All Compound Sources (Positive)
hyodeoxycholic acid	DGABKXLVXPYZII-SIBKNCMHSA-N	5283820	C24H40O4	392.2927		19	38	M-H2O+H, M+H, 2M+H, 2M+Na, M+Na, M-2H2O+H, M+K, M+H-H2O	ESI	Orbitrap, qTof	Isolated, commercial, crude, Commercial
Conjugated linoleic acid	JBYXPOFIGCOSSB-XBLVEGMJSA-N	5282796	C18H32O2	280.2402		8	15	M+H, M+H-H2O	ESI	Ion Trap, qTof	Isolated
Indole-3-lactic acid	XGILAAMKEQUXLS-UHFFFAOYSA-N	92904	C11H11NO3	205.0739		52	29	M+H, M+K, M+H-H2O, M-H2O+H	ESI, Positive, LC-ESI	Quattro_QQQ:40eV, Quattro_QQQ:25eV, Ion Trap, qTof, Orbitrap, Quattro_QQQ:10eV	Isolated, isolated, Commercial, NIH Natural Product Library
Tryptophan	QIVBCDIJIAJPQS-VIFPVBQESA-N	6305	C11H12N2O2	204.0899		221	160	M+H, [M+H-H2O]+, [M+Na]+, [M+K]+, [M+H]+, 2M+H, [M+H], M+Na	ESI, DI-ESI, Positive, LC-ESI	QQQ, Q-Exactive Plus, LC-ESI-ITFT, Quattro_QQQ:25eV, Ion Trap, Quattro_QQQ:40eV, qTof, Flow-injection QqQ/MS, Orbitrap, Quattro_QQQ:10eV, Hybrid FT, LC-ESI-QTOF, LC-Q-TOF/MS	Other, Isolated, Commercial standard, isolated, Crude, Commercial
Indopropionic acid	GOLXRNDWAUTYKT-UHFFFAOYSA-N	3744	C11H11NO2	189.079		39	49	M+H, M-H2O+H, M+H-H2O	ESI, Positive, LC-ESI	Quattro_QQQ:40eV, Quattro_QQQ:25eV, Ion Trap, qTof, Orbitrap, Quattro_QQQ:10eV	Isolated, Commercial, isolated
Indole-3-propionic acid	GOLXRNDWAUTYKT-UHFFFAOYSA-N	3744	C11H11NO2	189.079		39	49	M+H, M-H2O+H, M+H-H2O	ESI, Positive, LC-ESI	Quattro_QQQ:40eV, Quattro_QQQ:25eV, Ion Trap, qTof, Orbitrap, Quattro_QQQ:10eV	Isolated, Commercial, isolated
4-hydroxyphenyllactic acid	JVGVDSSUAVXRDY-UHFFFAOYSA-N	9378	C9H10O4	182.0579		22	53	M-H2O+H, M+H, [M+H]+, [M+H], M+Na	ESI, Positive	QQQ, Quattro_QQQ:40eV, Quattro_QQQ:25eV, qTof, Flow-injection QqQ/MS, Orbitrap, Quattro_QQQ:10eV, LC-Q-TOF/MS	Isolated, Commercial, isolated
Hippuric acid	QIAFMBKCNZACKA-UHFFFAOYSA-N	464	C9H9NO3	179.0582		90	105	M+H, [M+H]+, 2M+H, [M+H], M+Na	ESI, LC-ESI	QQQ, Q-Exactive Plus, Ion Trap, qTof, Flow-injection QqQ/MS, Orbitrap	Isolated, Commercial standard, isolated, Crude, Commercial
Serotonin	QZAYGJVTTNCVMB-UHFFFAOYSA-N	5202	C10H12N2O	176.095		85	7	M+H, [M+H-H2O]+, [M+Na]+, [M+K]+, [M+H]+, 2M+H, [M+H], M+Na	ESI, Positive, LC-ESI	QQQ, Q-Exactive Plus, Quattro_QQQ:40eV, Quattro_QQQ:25eV, qTof, Flow-injection QqQ/MS, Orbitrap, Quattro_QQQ:10eV, LC-ESI-QTOF, LC-Q-TOF/MS	, Isolated, Commercial standard, isolated, Crude, Commercial
3-3-PPA	QVWAEZJXDYOKEH-UHFFFAOYSA-N	91	C9H10O3	166.063		0	18
D-phenyllactic acid	VOXXWSYKYCBWHO-QMMMGPOBSA-N	444718	C9H10O3	166.063		22	68	M+H, M+K, [M+H], [M]+	ESI, Positive	Quattro_QQQ:40eV, Quattro_QQQ:25eV, qTof, Flow-injection QqQ/MS, Orbitrap, Quattro_QQQ:10eV	Crude, Isolated, Commercial, isolated
Glutamate	WHUUTDBJXJRKMK-VKHMYHEASA-N	33032	C5H9NO4	147.0532		196	86	M+H, [M+H-H2O]+, [M+H]+, 2M+H, [M+H], M-H+2Na, M+H-H2O	ESI, DI-ESI, Positive, LC-ESI	QQQ, Quattro_QQQ:40eV, LC-ESI-ITFT, Quattro_QQQ:25eV, qTof, Flow-injection QqQ/MS, Orbitrap, LC-ESI-QQ, Quattro_QQQ:10eV, LC-ESI-QTOF, LC-Q-TOF/MS	Lysate, Isolated, isolated, Crude, Commercial
alpha-hydroxyisocaproate	LVRFTAZAXQPQHI-UHFFFAOYSA-N	92779	C6H12O3	132.0786		7	28	M+H, [M+H]	ESI, Positive	Quattro_QQQ:40eV, Quattro_QQQ:25eV, Flow-injection QqQ/MS, Orbitrap, Quattro_QQQ:10eV, LC-Q-TOF/MS	Isolated, isolated
2-hydroxy-3-methylvalerate	RILPIWOPNGRASR-RFZPGFLSSA-N	10796774	C6H12O3	132.0786		0	4
alpha-hydroxyisovalerate	NGEWQZIDQIYUNV-UHFFFAOYSA-N	99823	C5H10O3	118.063		1	22	[M+H]	ESI	Flow-injection QqQ/MS	Isolated
Succinate	KDYFGRWQOYBRFD-UHFFFAOYSA-L	160419	C4H4O4-2	116.011		7	52	M+H, [M+H], M+H-H2O	ESI, LC-ESI	QQQ, qTof, Flow-injection QqQ/MS, Orbitrap, LC-Q-TOF/MS	Isolated, Commercial, isolated
Histamine	NTYJJOPFIAHURM-UHFFFAOYSA-N	774	C5H9N3	111.0796		50	3	M+H, [M+H], M+Na, [M+H]+	ESI, Positive, LC-ESI	QQQ, Q-Exactive Plus, Quattro_QQQ:40eV, Quattro_QQQ:25eV, qTof, Flow-injection QqQ/MS, Orbitrap, Quattro_QQQ:10eV, LC-Q-TOF/MS	Isolated, Commercial standard, Commercial, isolated
3-hydroxybutyric acid	WHBMMWSBFZVSSR-UHFFFAOYSA-N	441	C4H8O3	104.0473		11	43	M+H, [M+H], [M+H]+	ESI	QQQ, LC-ESI-IT, qTof, Flow-injection QqQ/MS, Orbitrap, LC-Q-TOF/MS	Isolated, isolated
GABA	BTCSSZJGUNDROE-UHFFFAOYSA-N	119	C4H9NO2	103.0633		61	16	M+H, [M+H]+, [M+H], M-H+2Na, M+H-H2O	ESI, Positive, LC-ESI	Q-Exactive Plus, QQQ, LC-ESI-ITFT, Quattro_QQQ:40eV, Quattro_QQQ:25eV, qTof, Flow-injection QqQ/MS, Orbitrap, LC-ESI-QQ, Quattro_QQQ:10eV, LC-ESI-QTOF, LC-Q-TOF/MS	Isolated, Commercial standard, Commercial, isolated
Lactic acid	JVTAAEKCZFNVCJ-UHFFFAOYSA-N	612	C3H6O3	90.0317		10	34	M+H, [M+H]	ESI	LC-Q-TOF/MS, Orbitrap, QQQ, Flow-injection QqQ/MS	Isolated
TMAO	UYPYRKYUKCHHIB-UHFFFAOYSA-N	1145	C3H9NO	75.0684		27	0	M+H, [M+H], [M+H]+	ESI, Positive	QQQ, Quattro_QQQ:40eV, Quattro_QQQ:25eV, qTof, Flow-injection QqQ/MS, Orbitrap, LC-ESI-QQ, Quattro_QQQ:10eV, LC-ESI-QTOF, LC-Q-TOF/MS	Isolated, isolated
Propionate	XBDQKXXYIPTUBI-UHFFFAOYSA-M	104745	C3H5O2-	73.029		381	6	M+H, [M+Na]+, [M+H]+	ESI, Positive	Quattro_QQQ:10eV, Quattro_QQQ:25eV, Orbitrap, Quattro_QQQ:40eV	Isolated, Commercial standard
TMA	GETQZCLCWQTVFV-UHFFFAOYSA-N	1146	C3H9N	59.0735		9	0	M+H	ESI, Positive	Quattro_QQQ:25eV, Orbitrap, Quattro_QQQ:10eV, Quattro_QQQ:40eV	Isolated
Acetate	QTBSBXVTEAMEQO-UHFFFAOYSA-M	175	C2H3O2-	59.0133		3	11	M+H	Positive	Quattro_QQQ:10eV, Quattro_QQQ:25eV, Quattro_QQQ:40eV	Isolated

from scripts.search_mzxml_for_ms2_by_precursor import main as search_mzxml_for_ms2_by_precursor
from scripts.metabolites_of_interest_gnps_library_lookup import create_df as create_metabolites_of_interest_gnps_library_lookup
from scripts.compare_search_results_to_gnps_library import run_in_parallel, load_gnps_library
from pathlib import Path
import os
import pickle 
import ast
import pickle
from scripts.mirror_plot import mirror_plot, plot_gnps_hits
import pandas as pd
import plotly.io as pio
pd.set_option('display.max_columns', None)
pd.set_option('display.width', 0) # Adjust display width if needed

# Get environment variables or use default values
TOP_DIR = os.getenv("TOP_DIR", ".")
CALC_DIR = Path(os.getenv("CALC_DIR", Path(TOP_DIR, "data", "calculated"))).resolve()
INTERMEDIATE_DIR = Path(os.getenv("INTERMEDIATE_DIR", Path(CALC_DIR, "intermediate"))).resolve()
MSV000084900_DIR = Path(os.getenv("MSV000084900_DIR", Path(TOP_DIR, "data/MSV000084900/v02"))).resolve()
GNPS2_RESULTS_DIR = Path(os.getenv("GNPS2_RESULTS_DIR", Path(TOP_DIR, "data/gnps2_results/18d82f1067e643538adf9b73147122c3"))).resolve()

CALC_DIR.mkdir(parents=True, exist_ok=True)
INTERMEDIATE_DIR.mkdir(parents=True, exist_ok=True)

# Check the directories
def check_top_dir(TOP_DIR=TOP_DIR):
    TOP_DIR = Path(TOP_DIR).resolve()
    if not TOP_DIR.exists():
        raise FileNotFoundError(f"Directory {TOP_DIR} does not exist.")
    with open(Path(TOP_DIR, "topdirvalidator"), "r") as f:
        line = f.readline()
        if line != "4a1b9837696299d80967925a0e49fff8":
            raise ValueError(f"Unexpected TOP_DIR: {TOP_DIR} ")   

def check_msv000084900_dir(MSV000084900_DIR=MSV000084900_DIR):
    if not MSV000084900_DIR.exists():
        raise FileNotFoundError(f"Directory {MSV000084900_DIR} does not exist.")

def check_gnps2_results_dir(GNPS2_RESULTS_DIR=GNPS2_RESULTS_DIR):
    # Check that clusterinfo.tsv exists
    if not Path(GNPS2_RESULTS_DIR, "nf_output/clustering/clusterinfo.tsv").exists():
        raise FileNotFoundError(f"Directory {GNPS2_RESULTS_DIR} does not exist.")

check_top_dir(TOP_DIR)
check_msv000084900_dir(MSV000084900_DIR)
check_gnps2_results_dir(GNPS2_RESULTS_DIR)

MOLECULE_OF_INTEREST=['2-hydroxy-3-methylvalerate','3-3-PPA','3-hydroxybutyric acid','hyodeoxycholic acid','4-hydroxyphenyllactic acid','Acetate','alpha-hydroxyisocaproate','Conjugated linoleic acid','D-phenyllactic acid','GABA','Glutamate','Hippuric acid','Histamine','Indole-3-lactic acid','Indole-3-propionic acid','Indopropionic acid','Lactic acid','Propionate','Serotonin','Succinate','TMAO','TMA','Tryptophan','alpha-hydroxyisovalerate']

Find all GNPS library entries that match the metabolites of interest

Given the names and PubChem CIDs of the metabolites of interest, find all matching entries in the GNPS public library via planar InChI Key.

create_metabolites_of_interest_gnps_library_lookup(
  json_path = Path(TOP_DIR, 'data', 'gnpslibrary.json'),
  outpath = Path(INTERMEDIATE_DIR, 'metabolites_of_interest_gnps_library_lookup.tsv')
)

GNPS2 Library Matches

Search by planar InChIKey

The results displayed are only the matches where the metabolite of interest has a corresponding entry in the GNPS library with the same planar InChIKey.

The tables are filtered results form spectra clustering by GNPS2 (nf_output/networking/clustersummary_with_network.tsv). Mirror plots are the GNPS library spectrum and the first entry in the GNPS2 cluster.

from IPython.display import display, HTML

df = pd.read_csv(Path(INTERMEDIATE_DIR, 'metabolites_of_interest_gnps_library_lookup.tsv'), sep='\t')
gnps_result_df = pd.read_csv(Path(GNPS2_RESULTS_DIR, 'nf_output/networking/clustersummary_with_network.tsv'), sep='\t', low_memory=False)
df['submatch_positive'] = df['submatch_positive'].apply(ast.literal_eval)
df['submatch_negative'] = df['submatch_negative'].apply(ast.literal_eval)
df['gnps_ids'] = df.apply(lambda row: [i['spectrum_id'] for i in row['submatch_positive']] + 
                                   [i['spectrum_id'] for i in row['submatch_negative']], axis=1)
df.drop(columns=['submatch_positive', 'submatch_negative'], inplace=True)

no_matches = []
for _, row in df.iterrows():
    tdf = gnps_result_df[gnps_result_df['SpectrumID'].isin(row['gnps_ids'])]
    if tdf.empty:
        no_matches.append(row['metabolite_of_interest'])
    else:
      print(f"### {row['metabolite_of_interest']}\n")
      display(HTML(tdf.to_html(index=False, classes='table')))
      if tdf.iloc[0]['SpectrumID'] not in MGF_DATA_DICT:
          print(f"Warning: SpectrumID {tdf.iloc[0]['SpectrumID']} not found in MGF_DATA_DICT\n")
          continue
      fig = plot_gnps_hits(
          tdf=tdf,
          mgf=MGF_DATA_DICT,
          GNPS2_RESULTS_DIR=GNPS2_RESULTS_DIR,
          MSV000084900_DIR=MSV000084900_DIR,
      )
      fig.show()

# Print metabolites with no matches
print("- **No matches found for the following metabolites:**")
for metabolite in no_matches:
    print(f"  - {metabolite}")

Indole-3-lactic acid

cluster index	number of spectra	parent mass	precursor charge	precursor mass	sum(precursor intensity)	RTMean	component	SpectrumID	#Scan#	SpectrumFile	LibraryName	MQScore	TIC_Query	RT_Query	MZErrorPPM	SharedPeaks	MassDiff	SpecMZ	SpecCharge	FileScanUniqueID	NumberHits	Compound_Name	Ion_Source	Instrument	Compound_Source	PI	Data_Collector	Adduct	Precursor_MZ	ExactMass	Charge	CAS_Number	Pubmed_ID	Smiles	INCHI	INCHI_AUX	Library_Class	IonMode	Organism	LibMZ	UpdateWorkflowName	LibraryQualityString	tags	molecular_formula	InChIKey	InChIKey-Planar	superclass	class	subclass	npclassifier_superclass	npclassifier_class	npclassifier_pathway	library_usi
2627	27	206.081	0	206.081	429935.0	3.290781	-1	CCMSLIB00003134667	2627.0	specs_ms.mgf	GNPS-NIST14-MATCHES.mgf	0.882585	23046.3	0.0	38.8709	5.0	0.008011	206.081	0.0	temp/specs_ms.mgf2627	1.0	Spectral Match to DL-Indole-3-lactic acid from NIST14	ESI	qTof	Isolated	Data from McKerrow	Data deposited by lamccall	M+H	206.089	205.074	1.0	832973	NaN	C1=CC=C2C(=C1)C(=CN2)CC(C(=O)O)O	InChI=1S/C11H11NO3/c13-10(11(14)15)5-7-6-12-9-4-2-1-3-8(7)9/h1-4,6,10,12-13H,5H2,(H,14,15)	NaN	3.0	Positive	GNPS-NIST14-MATCHES	206.089	UPDATE-SINGLE-ANNOTATED-BRONZE	Bronze	NaN	C11H11NO3	XGILAAMKEQUXLS-UHFFFAOYSA-N	XGILAAMKEQUXLS	Organoheterocyclic compounds	Indoles and derivatives	Indolyl carboxylic acids and derivatives	Tryptophan alkaloids	Simple indole alkaloids	Alkaloids	mzspec:GNPS:GNPS-LIBRARY:CCMSLIB00003134667

Tryptophan

cluster index	number of spectra	parent mass	precursor charge	precursor mass	sum(precursor intensity)	RTMean	component	SpectrumID	#Scan#	SpectrumFile	LibraryName	MQScore	TIC_Query	RT_Query	MZErrorPPM	SharedPeaks	MassDiff	SpecMZ	SpecCharge	FileScanUniqueID	NumberHits	Compound_Name	Ion_Source	Instrument	Compound_Source	PI	Data_Collector	Adduct	Precursor_MZ	ExactMass	Charge	CAS_Number	Pubmed_ID	Smiles	INCHI	INCHI_AUX	Library_Class	IonMode	Organism	LibMZ	UpdateWorkflowName	LibraryQualityString	tags	molecular_formula	InChIKey	InChIKey-Planar	superclass	class	subclass	npclassifier_superclass	npclassifier_class	npclassifier_pathway	library_usi
2550	2036	205.097	0	205.097	157104000.0	0.951604	3985	CCMSLIB00005778066	2550.0	specs_ms.mgf	MASSBANK.mgf	0.966012	240801.0	0.0	0.0	6.0	0.0	205.097	0.0	temp/specs_ms.mgf2550	1.0	Massbank:FIO00630 Tryptophan	ESI	qTof	Isolated	Massbank	Massbank	M+H	205.097	0.0	1.0	73-22-3	NaN	C1=CC=C2C(=C1)C(=CN2)C[C@@H](C(=O)O)N	1S/C11H12N2O2/c12-9(11(14)15)5-7-6-13-10-4-2-1-3-8(7)10/h1-4,6,9,13H,5,12H2,(H,14,15)/t9-/m0/s1	NaN	3.0	Positive	MASSBANK	205.097	UPDATE-SINGLE-ANNOTATED-BRONZE	Bronze	NaN	C11H12N2O2	QIVBCDIJIAJPQS-VIFPVBQESA-N	QIVBCDIJIAJPQS	Organoheterocyclic compounds	Indoles and derivatives	Indolyl carboxylic acids and derivatives	Small peptides	Aminoacids	Amino acids and Peptides|Shikimates and Phenylpropanoids	mzspec:GNPS:GNPS-LIBRARY:CCMSLIB00005778066

Hippuric acid

cluster index	number of spectra	parent mass	precursor charge	precursor mass	sum(precursor intensity)	RTMean	component	SpectrumID	#Scan#	SpectrumFile	LibraryName	MQScore	TIC_Query	RT_Query	MZErrorPPM	SharedPeaks	MassDiff	SpecMZ	SpecCharge	FileScanUniqueID	NumberHits	Compound_Name	Ion_Source	Instrument	Compound_Source	PI	Data_Collector	Adduct	Precursor_MZ	ExactMass	Charge	CAS_Number	Pubmed_ID	Smiles	INCHI	INCHI_AUX	Library_Class	IonMode	Organism	LibMZ	UpdateWorkflowName	LibraryQualityString	tags	molecular_formula	InChIKey	InChIKey-Planar	superclass	class	subclass	npclassifier_superclass	npclassifier_class	npclassifier_pathway	library_usi
659	10	180.066	0	180.066	2727860.0	1.456516	-1	CCMSLIB00005883437	659.0	specs_ms.mgf	GNPS-LIBRARY.mgf	0.965707	9691.8	0.0	0.0	5.0	0.0	180.066	0.0	temp/specs_ms.mgf659	1.0	HIPPURATE - 30.0 eV	ESI	Orbitrap	Isolated	Madeleine Ernst	Anna Abrahamsson	M+H	180.066	0.0	1.0	495-69-2	NaN	OC(=O)CNC(=O)C1=CC=CC=C1	InChI=1S/C9H9NO3/c11-8(12)6-10-9(13)7-4-2-1-3-5-7/h1-5H,6H2,(H,10,13)(H,11,12)	NaN	1.0	Positive	GNPS-LIBRARY	180.066	UPDATE-SINGLE-ANNOTATED-GOLD	Gold	NaN	C9H9NO3	QIAFMBKCNZACKA-UHFFFAOYSA-N	QIAFMBKCNZACKA	Benzenoids	Benzene and substituted derivatives	Benzoic acids and derivatives	Small peptides	Aminoacids	Amino acids and Peptides	mzspec:GNPS:GNPS-LIBRARY:CCMSLIB00005883437

Serotonin

cluster index	number of spectra	parent mass	precursor charge	precursor mass	sum(precursor intensity)	RTMean	component	SpectrumID	#Scan#	SpectrumFile	LibraryName	MQScore	TIC_Query	RT_Query	MZErrorPPM	SharedPeaks	MassDiff	SpecMZ	SpecCharge	FileScanUniqueID	NumberHits	Compound_Name	Ion_Source	Instrument	Compound_Source	PI	Data_Collector	Adduct	Precursor_MZ	ExactMass	Charge	CAS_Number	Pubmed_ID	Smiles	INCHI	INCHI_AUX	Library_Class	IonMode	Organism	LibMZ	UpdateWorkflowName	LibraryQualityString	tags	molecular_formula	InChIKey	InChIKey-Planar	superclass	class	subclass	npclassifier_superclass	npclassifier_class	npclassifier_pathway	library_usi
594	6	177.102	0	177.102	249916.0	0.471619	-1	CCMSLIB00003134728	594.0	specs_ms.mgf	GNPS-NIST14-MATCHES.mgf	0.807959	5647.54	0.0	0.0	6.0	0.0	177.102	0.0	temp/specs_ms.mgf594	1.0	Spectral Match to Serotonin from NIST14	ESI	qTof	Isolated	Data from Jairam KP Vanamala, PhD	Data deposited by mjmeehan	M+H	177.102	176.095	1.0	50679	NaN	C1=CC2=C(C=C1O)C(=CN2)CCN	InChI=1S/C10H12N2O/c11-4-3-7-6-12-10-2-1-8(13)5-9(7)10/h1-2,5-6,12-13H,3-4,11H2	NaN	3.0	Positive	GNPS-NIST14-MATCHES	177.102	UPDATE-SINGLE-ANNOTATED-BRONZE	Bronze	NaN	C10H12N2O	QZAYGJVTTNCVMB-UHFFFAOYSA-N	QZAYGJVTTNCVMB	Organoheterocyclic compounds	Indoles and derivatives	Tryptamines and derivatives	Tryptophan alkaloids	Simple indole alkaloids	Alkaloids	mzspec:GNPS:GNPS-LIBRARY:CCMSLIB00003134728

• No matches found for the following metabolites:
  • hyodeoxycholic acid
  • Conjugated linoleic acid
  • Indopropionic acid
  • Indole-3-propionic acid
  • 4-hydroxyphenyllactic acid
  • 3-3-PPA
  • D-phenyllactic acid
  • Glutamate
  • alpha-hydroxyisocaproate
  • 2-hydroxy-3-methylvalerate
  • Succinate
  • Histamine
  • 3-hydroxybutyric acid
  • GABA
  • Lactic acid
  • TMAO
  • Propionate
  • TMA
  • Acetate
  • alpha-hydroxyisovalerate

Manual examination of GNPS2 search results

CCMSLIB00003138284 371 specs_ms.mgf GNPS-NIST14-MATCHES.mgf 0.863861 10861.2 0 0 5 0 165.055 0 temp/specs_ms.mgf371 1 Spectral Match to p-Hydroxyphenyllactic acid from NIST14 CCMSLIB00010010644 8345 specs_ms.mgf ECG-ACYL-AMIDES-C4-C24-LIBRARY.mgf 0.986215 8975.94 0 4.16397 6 0.000991821 238.19 0 temp/specs_ms.mgf8345 1 histamine-C8:0

gnps_result_df = pd.read_csv(Path(GNPS2_RESULTS_DIR, 'nf_output/networking/clustersummary_with_network.tsv'), sep='\t', low_memory=False)
tdf = gnps_result_df[gnps_result_df['SpectrumID'].isin(['CCMSLIB00003138284'])]
print("### 4-hydroxyphenyllactic acid")
display(HTML(tdf.to_html(index=False, classes='table')))
fig = plot_gnps_hits(
          tdf=tdf,
          mgf=MGF_DATA_DICT,
          GNPS2_RESULTS_DIR=GNPS2_RESULTS_DIR,
          MSV000084900_DIR=MSV000084900_DIR,
      )
fig.show()

4-hydroxyphenyllactic acid

cluster index	number of spectra	parent mass	precursor charge	precursor mass	sum(precursor intensity)	RTMean	component	SpectrumID	#Scan#	SpectrumFile	LibraryName	MQScore	TIC_Query	RT_Query	MZErrorPPM	SharedPeaks	MassDiff	SpecMZ	SpecCharge	FileScanUniqueID	NumberHits	Compound_Name	Ion_Source	Instrument	Compound_Source	PI	Data_Collector	Adduct	Precursor_MZ	ExactMass	Charge	CAS_Number	Pubmed_ID	Smiles	INCHI	INCHI_AUX	Library_Class	IonMode	Organism	LibMZ	UpdateWorkflowName	LibraryQualityString	tags	molecular_formula	InChIKey	InChIKey-Planar	superclass	class	subclass	npclassifier_superclass	npclassifier_class	npclassifier_pathway	library_usi
371	12	165.055	0	165.055	1055820.0	1.524683	7747	CCMSLIB00003138284	371.0	specs_ms.mgf	GNPS-NIST14-MATCHES.mgf	0.863861	10861.2	0.0	0.0	5.0	0.0	165.055	0.0	temp/specs_ms.mgf371	1.0	Spectral Match to p-Hydroxyphenyllactic acid from NIST14	ESI	HCD	Isolated	Data from Jairam KP Vanamala, PhD	Data deposited by mjmeehan	M+H-H2O	165.055	0.0	1.0	306230	NaN	NaN	NaN	NaN	3.0	Positive	GNPS-NIST14-MATCHES	165.055	UPDATE-SINGLE-ANNOTATED-BRONZE	Bronze	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	mzspec:GNPS:GNPS-LIBRARY:CCMSLIB00003138284

gnps_result_df = pd.read_csv(Path(GNPS2_RESULTS_DIR, 'nf_output/networking/clustersummary_with_network.tsv'), sep='\t', low_memory=False)
tdf = gnps_result_df[gnps_result_df['SpectrumID'].isin(['CCMSLIB00010010644'])]
print('### Histamine-C8:0')
display(HTML(tdf.to_html(index=False, classes='table')))
fig = plot_gnps_hits(
          tdf=tdf,
          mgf=MGF_DATA_DICT,
          GNPS2_RESULTS_DIR=GNPS2_RESULTS_DIR,
          MSV000084900_DIR=MSV000084900_DIR,
      )
fig.show()

Histamine-C8:0

cluster index	number of spectra	parent mass	precursor charge	precursor mass	sum(precursor intensity)	RTMean	component	SpectrumID	#Scan#	SpectrumFile	LibraryName	MQScore	TIC_Query	RT_Query	MZErrorPPM	SharedPeaks	MassDiff	SpecMZ	SpecCharge	FileScanUniqueID	NumberHits	Compound_Name	Ion_Source	Instrument	Compound_Source	PI	Data_Collector	Adduct	Precursor_MZ	ExactMass	Charge	CAS_Number	Pubmed_ID	Smiles	INCHI	INCHI_AUX	Library_Class	IonMode	Organism	LibMZ	UpdateWorkflowName	LibraryQualityString	tags	molecular_formula	InChIKey	InChIKey-Planar	superclass	class	subclass	npclassifier_superclass	npclassifier_class	npclassifier_pathway	library_usi
8345	9	238.19	0	238.19	1325900.0	4.124967	9461	CCMSLIB00010010644	8345.0	specs_ms.mgf	ECG-ACYL-AMIDES-C4-C24-LIBRARY.mgf	0.986215	8975.94	0.0	4.16397	6.0	0.000992	238.19	0.0	temp/specs_ms.mgf8345	1.0	histamine-C8:0	ESI	qTof	Crude	Dorrestein	Emily Gentry	M+H	238.191	237.184	1.0	NaN	NaN	CCCCCCCC(NCCC1=NC=CN1)=O	InChI=1S/C13H23N3O/c1-2-3-4-5-6-7-13(17)16-9-8-12-14-10-11-15-12/h10-11H,2-9H2,1H3,(H,14,15)(H,16,17)	NaN	2.0	Positive	ECG-ACYL-AMIDES-C4-C24-LIBRARY	238.191	UPDATE-SINGLE-ANNOTATED-SILVER	Silver	NaN	C13H23N3O	OFFGMPVWGIKLDD-UHFFFAOYSA-N	OFFGMPVWGIKLDD	Lipids and lipid-like molecules	Fatty Acyls	Fatty amides	Histidine alkaloids	Imidazole alkaloids	Alkaloids	mzspec:GNPS:GNPS-LIBRARY:CCMSLIB00010010644